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Karthik Shekhar - Publications

Affiliations: 
UC Berkeley, MIT 
Area:
Single-cell genomics, retina, neuron electrochemistry
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30 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Allen AE, Hahn J, Richardson R, Pantiru A, Mouland J, Baño-Otalora B, Monavarfeshani A, Yan W, Williams C, Wynne J, Rodgers J, Milosavljevic N, Orlowska-Feuer P, Storchi R, Sanes JR, ... Shekhar K, et al. Reconfiguration of the visual code and retinal cell type complement in closely related diurnal and nocturnal mice. Biorxiv : the Preprint Server For Biology. PMID 38915685 DOI: 10.1101/2024.06.14.598659  0.502
2024 Hellevik AM, Mardoum P, Hahn J, Kölsch Y, D'Orazi FD, Suzuki SC, Godinho L, Lawrence O, Rieke F, Shekhar K, Sanes JR, Baier H, Baden T, Wong RO, Yoshimatsu T. Ancient origin of the rod bipolar cell pathway in the vertebrate retina. Nature Ecology & Evolution. PMID 38627529 DOI: 10.1038/s41559-024-02404-w  0.511
2023 Xie F, Jain S, Butrus S, Shekhar K, Zipursky SL. Vision sculpts a continuum of L2/3 cell types in the visual cortex during the critical period. Biorxiv : the Preprint Server For Biology. PMID 38187533 DOI: 10.1101/2023.12.18.572244  0.623
2023 Hahn J, Monavarfeshani A, Qiao M, Kao AH, Kölsch Y, Kumar A, Kunze VP, Rasys AM, Richardson R, Wekselblatt JB, Baier H, Lucas RJ, Li W, Meister M, Trachtenberg JT, ... ... Shekhar K, et al. Evolution of neuronal cell classes and types in the vertebrate retina. Nature. 624: 415-424. PMID 38092908 DOI: 10.1038/s41586-023-06638-9  0.629
2023 Chen R, Li J, Wang J, Ibarra I, Cheng X, Luecken M, Liu J, Monavarfeshani A, Yan W, Zheng Y, Zuo Z, Colborn S, Cortez B, Owen LA, Tran N, ... Shekhar K, et al. Integrated multi-omics single cell atlas of the human retina. Research Square. PMID 38014002 DOI: 10.21203/rs.3.rs-3471275/v1  0.504
2023 Yoshimatsu T, Mardoum P, Hahn J, Kolsch Y, Suzuki S, Godinho L, Lawrence O, Rieke F, Shekhar K, Sanes J, Baier H, Baden T, Wong R. Ancient origin of the rod bipolar cell pathway in the vertebrate retina. Research Square. PMID 37886445 DOI: 10.21203/rs.3.rs-3411693/v1  0.529
2023 Hellevik AM, Mardoum P, Hahn J, Kölsch Y, D'Orazi FD, Suzuki SC, Godinho L, Lawrence O, Rieke F, Shekhar K, Sanes JR, Baier H, Baden T, Wong RO, Yoshimatsu T. Ancient origin of the rod bipolar cell pathway in the vertebrate retina. Biorxiv : the Preprint Server For Biology. PMID 37771914 DOI: 10.1101/2023.09.12.557433  0.536
2023 Hahn J, Monavarfeshani A, Qiao M, Kao A, Kölsch Y, Kumar A, Kunze VP, Rasys AM, Richardson R, Baier H, Lucas RJ, Li W, Meister M, Trachtenberg JT, Yan W, ... ... Shekhar K, et al. Evolution of neuronal cell classes and types in the vertebrate retina. Biorxiv : the Preprint Server For Biology. PMID 37066415 DOI: 10.1101/2023.04.07.536039  0.618
2023 Butrus S, Sagireddy S, Yan W, Shekhar K. Defining Selective Neuronal Resilience and Identifying Targets of Neuroprotection and Axon Regeneration Using Single-Cell RNA Sequencing: Computational Approaches. Methods in Molecular Biology (Clifton, N.J.). 2636: 19-41. PMID 36881293 DOI: 10.1007/978-1-0716-3012-9_2  0.408
2023 Benhar I, Ding J, Yan W, Whitney IE, Jacobi A, Sud M, Burgin G, Shekhar K, Tran NM, Wang C, He Z, Sanes JR, Regev A. Temporal single-cell atlas of non-neuronal retinal cells reveals dynamic, coordinated multicellular responses to central nervous system injury. Nature Immunology. PMID 36807640 DOI: 10.1038/s41590-023-01437-w  0.366
2022 Whitney IE, Butrus S, Dyer MA, Rieke F, Sanes JR, Shekhar K. Vision-Dependent and -Independent Molecular Maturation of Mouse Retinal Ganglion Cells. Neuroscience. PMID 35870562 DOI: 10.1016/j.neuroscience.2022.07.013  0.57
2022 Goetz J, Jessen ZF, Jacobi A, Mani A, Cooler S, Greer D, Kadri S, Segal J, Shekhar K, Sanes JR, Schwartz GW. Unified classification of mouse retinal ganglion cells using function, morphology, and gene expression. Cell Reports. 40: 111040. PMID 35830791 DOI: 10.1016/j.celrep.2022.111040  0.372
2022 Shekhar K, Whitney IE, Butrus S, Peng YR, Sanes JR. Diversification of multipotential postmitotic mouse retinal ganglion cell precursors into discrete types. Elife. 11. PMID 35191836 DOI: 10.7554/eLife.73809  0.517
2022 Cheng S, Butrus S, Tan L, Xu R, Sagireddy S, Trachtenberg JT, Shekhar K, Zipursky SL. Vision-dependent specification of cell types and function in the developing cortex. Cell. 185: 311-327.e24. PMID 35063073 DOI: 10.1016/j.cell.2021.12.022  0.522
2021 Shekhar K, Sanes JR. Generating and Using Transcriptomically Based Retinal Cell Atlases. Annual Review of Vision Science. PMID 34228938 DOI: 10.1146/annurev-vision-032621-075200  0.518
2020 Kölsch Y, Hahn J, Sappington A, Stemmer M, Fernandes AM, Helmbrecht TO, Lele S, Butrus S, Laurell E, Arnold-Ammer I, Shekhar K, Sanes JR, Baier H. Molecular classification of zebrafish retinal ganglion cells links genes to cell types to behavior. Neuron. PMID 33357413 DOI: 10.1016/j.neuron.2020.12.003  0.552
2020 Yan W, Peng YR, van Zyl T, Regev A, Shekhar K, Juric D, Sanes JR. Cell Atlas of The Human Fovea and Peripheral Retina. Scientific Reports. 10: 9802. PMID 32555229 DOI: 10.1038/S41598-020-66092-9  0.57
2020 van Zyl T, Yan W, McAdams A, Peng YR, Shekhar K, Regev A, Juric D, Sanes JR. Cell atlas of aqueous humor outflow pathways in eyes of humans and four model species provides insight into glaucoma pathogenesis. Proceedings of the National Academy of Sciences of the United States of America. PMID 32341164 DOI: 10.1073/Pnas.2001250117  0.559
2019 Tran NM, Shekhar K, Whitney IE, Jacobi A, Benhar I, Hong G, Yan W, Adiconis X, Arnold ME, Lee JM, Levin JZ, Lin D, Wang C, Lieber CM, Regev A, et al. Single-Cell Profiles of Retinal Ganglion Cells Differing in Resilience to Injury Reveal Neuroprotective Genes. Neuron. PMID 31784286 DOI: 10.1016/J.Neuron.2019.11.006  0.439
2019 Shekhar K, Menon V. Identification of Cell Types from Single-Cell Transcriptomic Data. Methods in Molecular Biology (Clifton, N.J.). 1935: 45-77. PMID 30758819 DOI: 10.1007/978-1-4939-9057-3_4  0.432
2019 Peng YR, Shekhar K, Yan W, Herrmann D, Sappington A, Bryman GS, van Zyl T, Do MTH, Regev A, Sanes JR. Molecular Classification and Comparative Taxonomics of Foveal and Peripheral Cells in Primate Retina. Cell. PMID 30712875 DOI: 10.1016/J.Cell.2019.01.004  0.594
2018 Biton M, Haber AL, Rogel N, Burgin G, Beyaz S, Schnell A, Ashenberg O, Su CW, Smillie C, Shekhar K, Chen Z, Wu C, Ordovas-Montanes J, Alvarez D, Herbst RH, et al. T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation. Cell. PMID 30392957 DOI: 10.1016/J.Cell.2018.10.008  0.393
2018 Moffitt JR, Bambah-Mukku D, Eichhorn SW, Vaughn E, Shekhar K, Perez JD, Rubinstein ND, Hao J, Regev A, Dulac C, Zhuang X. Molecular, spatial and functional single-cell profiling of the hypothalamic preoptic region. Science (New York, N.Y.). PMID 30385464 DOI: 10.1126/Science.Aau5324  0.367
2018 Farrell JA, Wang Y, Riesenfeld SJ, Shekhar K, Regev A, Schier AF. Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis. Science (New York, N.Y.). PMID 29700225 DOI: 10.1126/Science.Aar3131  0.46
2018 Pandey S, Shekhar K, Regev A, Schier AF. Comprehensive Identification and Spatial Mapping of Habenular Neuronal Types Using Single-Cell RNA-Seq. Current Biology : Cb. PMID 29576475 DOI: 10.1016/j.cub.2018.02.040  0.425
2018 Villani AC, Shekhar K. Single-Cell RNA Sequencing of Human T Cells. Methods in Molecular Biology (Clifton, N.J.). 1514: 203-239. PMID 27787803 DOI: 10.1007/978-1-4939-6548-9_16  0.387
2017 Haber AL, Biton M, Rogel N, Herbst RH, Shekhar K, Smillie C, Burgin G, Delorey TM, Howitt MR, Katz Y, Tirosh I, Beyaz S, Dionne D, Zhang M, Raychowdhury R, et al. A single-cell survey of the small intestinal epithelium. Nature. 551: 333-339. PMID 29144463 DOI: 10.1038/Nature24489  0.452
2016 Shekhar K, Lapan SW, Whitney IE, Tran NM, Macosko EZ, Kowalczyk M, Adiconis X, Levin JZ, Nemesh J, Goldman M, McCarroll SA, Cepko CL, Regev A, Sanes JR. Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics. Cell. 166: 1308-1323.e30. PMID 27565351 DOI: 10.1016/J.Cell.2016.07.054  0.429
2015 Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, Tirosh I, Bialas AR, Kamitaki N, Martersteck EM, Trombetta JJ, Weitz DA, Sanes JR, Shalek AK, Regev A, et al. Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell. 161: 1202-14. PMID 26000488 DOI: 10.1016/J.Cell.2015.05.002  0.526
2014 Shekhar K, Brodin P, Davis MM, Chakraborty AK. Automatic Classification of Cellular Expression by Nonlinear Stochastic Embedding (ACCENSE). Proceedings of the National Academy of Sciences of the United States of America. 111: 202-7. PMID 24344260 DOI: 10.1073/Pnas.1321405111  0.327
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